[SalesForce] Marketing Cloud Automation studio won’t update data extension

We are having trouble updating records in a data extension from an automation. It creates new records but it won't update. We have the salesforce custom object ID set up as the primary key and the subscriber key linked up in the extension. We then run a SQL activity in the automation studio which "Updates" the data extension, but it doesn't update existing record, it just adds any new ones.

Can anyone help please?

Many Thanks

**** Edit ****

So here is my data extension, the ID is set to the primary key. I can't use the subscriberKey because it is a one to many relationship so there would be multiple records with the same subscriberkey in this data extension

My SOQL that is used in the automation to populate the data extension.

Select id,
Buyer_Type__c as PlotID ,
Developments__c as DevelopmentID, 
Region__c as RegionID, 
Lead__c as SubscriberKey, 
Customer_Email__c as EmailAddress,
Status__c as Status, 
Record_Type_Name__c as RecordType 
from Interest__c_Salesforce 
where Status__c = 'Active'